Question: edgeR Normalization Method
0
3.7 years ago by
p_das0
United States
p_das0 wrote:

Hi

Can anybody point out to a tutorial/paper which explains the normalization method used by edgeR?

Another thing, though, TMM is the default normalization method of edgeR, can one specify, any other normalization methods in edgeR?

Thank you!

Prerna

edger • 3.8k views
modified 3.7 years ago by Ryan C. Thompson7.3k • written 3.7 years ago by p_das0

When I say TMM paper...it is excluding the Genome Biology TMM paper by Robinson and Oshlack...

4

What's wrong with the Genome Biology paper? That describes the TMM method called by calcNormFactors with its default settings. You're not going to get anything more descriptive than that.

Hi Aaron!

Nothing is wrong!! Just wanted to see if there are more write ups on TMM...No offense to the authors or the research group...

P

1

See Dillies et al. 2012 for a comparison of different normalization methods: http://bib.oxfordjournals.org/content/early/2012/09/15/bib.bbs046

edgeR's TMM and DESeq's method come out on top.

Jenny

2
3.7 years ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson7.3k wrote:

The documentation for calcNormFactors describes the options for the method argument, which allows you to select 3 different normalization methods. In addition, you can calculate normalization factors by any method you like and store them in the DGEList object yourself under object$samples$norm.factors.